lammps错误诊断8-Out of range atoms - cannot compute PPPM

2018/12/22 15:49
阅读数 6.7K

错误“Out of range atoms - cannot compute PPPM (../pppm.cpp:1937)”的典型报告为:

---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =           -nan KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =           -nan E_bond   =      5536.5700 E_angle  =           -nan 
E_dihed  =       405.0252 E_impro  =       799.1751 E_vdwl   =           -nan 
E_coul   =           -nan E_long   =     -2301.2059 Press    =           -nan 
ERROR on proc 8: Out of range atoms - cannot compute PPPM (../pppm.cpp:1937)
ERROR on proc 15: Out of range atoms - cannot compute PPPM (../pppm.cpp:1937)

这一步显示后,就exit了。目前来讲,似乎唯一可行的方案就是调整原子的初始构型(不合理的初始构型会导致局部的受力太大),时间步调小或者 negibor list 增大基本不凑效。这种调整构型手工很难办成,即使是利用最小化的方案,一般也不宜用同一种力场来进行调整。下面这个调整就是在ChemBio3D 下利用MM2最小化完成的,效果还不错:

There is no secondary-structure information recorded.
Bond length is unusually long: 4.79754 223-222
Bond length is unusually long: 2.70009 328-327
Bond length to Hydrogen is unusually long: 2.13469 456-457
Bond length to Hydrogen is unusually long: 2.13561 456-458

Since there is no secondary-structure information, ChemBio3D Ultra is going to formcompute it.
The number of atoms in this molecule exceeds the atom synchronization limit. The ChemDraw panel cannot load the molecular structure.
MM2 Calculation completed successfully
------------MM2 Minimization------------
Warning: The number of ligands attached does not match the geometry of N(1)
Warning: The number of ligands attached does not match the geometry of O(139)
Warning: The number of ligands attached does not match the geometry of O(453)
Warning: The number of ligands attached does not match the geometry of C(457)
Warning: The number of ligands attached does not match the geometry of H(458)
Warning: The number of ligands attached does not match the geometry of H(459)
Warning: The number of ligands attached does not match the geometry of C(559)
Separating coincident atoms: C(63)-H(64)
Separating coincident atoms: C(238)-H(239)
Pi System:  538 536 534 533 541 543
Warning: Some parameters are guessed (Quality = 1).
  Iteration    1  Steric Energy 274941803.943  RMS Gradient 1341504.134  RMS Move   0.0000
  Iteration    2  Steric Energy 104634145.547  RMS Gradient 628201.522  RMS Move   0.0892
  Iteration    3  Steric Energy 98644711.696  RMS Gradient 619854.158  RMS Move   0.0223
  Iteration    4  Steric Energy 36519658.997  RMS Gradient 278060.506  RMS Move   0.0717
  Iteration    5  Steric Energy 33726135.351  RMS Gradient 272796.212  RMS Move   0.0223
  Iteration    6  Steric Energy 14471590.989  RMS Gradient 125631.455  RMS Move   0.0497
  Iteration    7  Steric Energy 13180439.253  RMS Gradient 125367.907  RMS Move   0.0223
------------------------------------------------------------------
Iteration 6205  Steric Energy -157.182  RMS Gradient    0.015  RMS Move   0.0000
  Iteration 6206  Steric Energy -157.182  RMS Gradient    0.011  RMS Move   0.0000
  Iteration 6207  Steric Energy -157.182  RMS Gradient    0.009  RMS Move   0.0000
  Iteration 6207: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
  Stretch:               25.2323
  Bend:                 288.0828
  Stretch-Bend:          -1.1579
  Torsion:              141.6311
  Non-1,4 VDW:         -380.2947
  1,4 VDW:              148.6268
  Dipole/Dipole:       -379.3025
Total Energy:          -157.1821 kcal/mol
Calculation ended

该步骤不仅指出了原因,也给出了迭代步骤,最后还计算了各种能量的大小。在完成这个初步调整的基础上,我们比较了一下两种结构的差别:

其中黄色是调整前的不理想的初始结构,绿色是在此基础上利用MM2力场调整的结构。通过这个步骤输出的pdb文件就可以在lammps里面顺利运行了:

---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =      6842.2689 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =      6842.2689 E_bond   =      5217.8375 E_angle  =       889.2725 
E_dihed  =       220.4900 E_impro  =         1.9840 E_vdwl   =       373.2779 
E_coul   =      2417.1047 E_long   =     -2277.6976 Press    =    -10629.6498 
---------------- Step       10 ----- CPU =      0.0337 (sec) ----------------
TotEng   =      2472.8837 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =      2472.8837 E_bond   =      1476.8188 E_angle  =       611.9309 
E_dihed  =       226.6634 E_impro  =         2.8918 E_vdwl   =        31.9095 
E_coul   =      2405.3611 E_long   =     -2282.6917 Press    =     -3317.6592 
---------------- Step       20 ----- CPU =      0.0562 (sec) ----------------
TotEng   =       998.0748 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =       998.0748 E_bond   =       200.8747 E_angle  =       453.3712 
E_dihed  =       234.2443 E_impro  =         6.1779 E_vdwl   =        -6.6921 
E_coul   =      2397.4972 E_long   =     -2287.3984 Press    =      1691.6034

通过这个初始结构的运行结构对比,还可以进一步启发对于蛋白质链自相互作用机理的研究,这里暂不赘述。

 

参考链接:

[1] lammps运行一段时间ERROR on proc 0: Out of range atoms - cannot compute PPPM

[2] Re: [lammps-users] Error on proc 0: Out of range atoms - cannot compute PPPM

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